[BioC] NCBI gff3 annotation file and read.gff()

[Ugo Borello]

Hi,

I am trying to read without success, a gff file downloaded from the NCBI
genomes ftp directory.

library("genomes")
> annot <- 
read.gff('~/Desktop/NCBI_Anno/ref_Macaca_fascicularis_5.0_top_level.gff3')
Error in `$<-.data.frame`(`*tmp*`, "description", value = "") :
  replacement has 1 row, data has 0

Any hint/help?

Thank you

Ugo




> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods
base     

other attached packages:
 [1] genomes_2.10.0       Biostrings_2.32.1    XVector_0.4.0
GenomicRanges_1.16.3 GenomeInfoDb_1.0.2
 [6] IRanges_1.22.9       BiocGenerics_0.10.0  RCurl_1.95-4.1
bitops_1.0-6         XML_3.98-1.1

loaded via a namespace (and not attached):
[1] stats4_3.1.1    tools_3.1.1     zlibbioc_1.10.0